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Supported Data Types

This page will list the bioinformatics and chemistry data formats which Bioclipse 1.0 will support.


Supported = Ability to read and write and interpret as a parsed BioResource

  • Chemical Markup Language (.cml)
  • Jmol script (.scr, .spt)
  • JCAMP-DX (jx, jdx)
  • Ghemical (gpr) [post 1.0]
  • MDL Molfile format (mol)
  • MDL SDFile [post 1.0]
  • HIN
  • XYZ
  • Mol2 [post 1.0]
  • CIF [post 1.0]
  • MDL RXN [post 1.0]


  • PDB
  • Fasta
  • PDB-ML post 1.0
  • mmCIF post 1.0


Roundtripping is the process where molecular content is saved into a file and read again. During roundtripping information is supposed to be preserved. Tests for this in CDK are ongoing.